Index: trunk/DOC/TexFiles/Chapters/Introduction.tex
===================================================================
--- trunk/DOC/TexFiles/Chapters/Introduction.tex	(revision 2531)
+++ trunk/DOC/TexFiles/Chapters/Introduction.tex	(revision 2541)
@@ -41,14 +41,14 @@
 the tendency terms of the equations are evaluated either centered  in time, or forward, 
 or backward depending of the nature of the term.
-Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered grid 
-(Arakawa C grid) with masking of land areas and uses a Leap-frog environment for time-stepping. 
-Vertical discretisation used depends on both how the bottom topography is represented and 
-whether the free surface is linear or not. Full step or partial step $z$-coordinate or 
-$s$- (terrain-following) coordinate is used with linear free surface (level position are then 
-fixed in time). In non-linear free surface, the corresponding rescaled height coordinate 
-formulation (\textit{z*} or \textit{s*}) is used (the level position then vary in time as a 
-function of the sea surface heigh). The following two chapters (\ref{TRA} and \ref{DYN}) 
-describe the discretisation of the prognostic equations for the active tracers and the 
-momentum. Explicit, split-explicit and filtered free surface formulations are implemented. 
+Chapter~\ref{DOM} presents the space domain. The model is discretised on a staggered 
+grid (Arakawa C grid) with masking of land areas. Vertical discretisation used depends 
+on both how the bottom topography is represented and whether the free surface is linear or not. 
+Full step or partial step $z$-coordinate or $s$- (terrain-following) coordinate is used 
+with linear free surface (level position are then fixed in time). In non-linear free surface, 
+the corresponding rescaled height coordinate formulation (\textit{z*} or \textit{s*}) is used 
+(the level position then vary in time as a function of the sea surface heigh). 
+The following two chapters (\ref{TRA} and \ref{DYN}) describe the discretisation of the 
+prognostic equations for the active tracers and the momentum. Explicit, split-explicit 
+and filtered free surface formulations are implemented. 
 A number of numerical schemes are available for momentum advection, for the computation 
 of the pressure gradients, as well as for the advection of tracers (second or higher 
@@ -79,12 +79,16 @@
 or \citet{Umlauf_Burchard_JMS03} mixing schemes.
 
-Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature and salinity, 
-sea surface temperature, sea level anomaly and sea ice concentration) and calculates an interpolated 
-model equivalent value at the observation location and nearest model timestep. Originally 
-developed of data assimilation, it is a fantastic tool for model and data comparison.
-Other Specific online diagnostics (not documented yet) are available in the model: output of all 
-the tendencies of the momentum and tracers equations, output of tracers tendencies 
-averaged over the time evolving mixed layer, output of the tendencies of the barotropic 
-vorticity equation, on-line floats trajectories...
+Model outputs management and specific online diagnostics are described in chapters~\ref{DIA}.
+The diagnostics includes the output of all the tendencies of the momentum and tracers equations, 
+the output of tracers tendencies averaged over the time evolving mixed layer, the output of 
+the tendencies of the barotropic vorticity equation, the computation of on-line floats trajectories... 
+Chapter~\ref{OBS} describes a tool which reads in observation files (profile temperature 
+and salinity, sea surface temperature, sea level anomaly and sea ice concentration) 
+and calculates an interpolated model equivalent value at the observation location 
+and nearest model timestep. Originally developed of data assimilation, it is a fantastic 
+tool for model and data comparison. Chapter~\ref{ASM} describes how increments 
+produced by data assimilation may be applied to the model equations.
+Finally, Chapter~\ref{CFG} provides a brief introduction to the pre-defined model 
+configurations (water column model, ORCA and GYRE families of configurations).
 
 The model is implemented in \textsc{Fortran 90}, with preprocessing (C-pre-processor). 
@@ -102,5 +106,5 @@
 around the code, the module names follow a three-letter rule. For example, \mdl{traldf} 
 is a module related to the TRAcers equation, computing the Lateral DiFfussion. 
-The complete list of module names is presented in Appendix~\ref{Apdx_D}. 
+%The complete list of module names is presented in Appendix~\ref{Apdx_D}.      %====>>>> to be done !
 Furthermore, modules are organized in a few directories that correspond to their category, 
 as indicated by the first three letters of their name (Tab.~\ref{Tab_chap}). 
@@ -114,4 +118,5 @@
 \begin{table}[!t]	
 %\begin{center} \begin{tabular}{|p{143pt}|l|l|}	\hline
+\caption{ \label{Tab_chap}   Organization of Chapters mimicking the one of the model directories. }
 \begin{center} 	\begin{tabular}{|l|l|l|}	\hline
 Chapter \ref{STP}	& -   		        & model time STePping environment \\		\hline
@@ -123,12 +128,10 @@
 Chapter \ref{LDF}	& LDF		& Lateral DiFfusion (parameterisations) \\	\hline
 Chapter \ref{ZDF}	& ZDF		& vertical (Z) DiFfusion (parameterisations)  \\		\hline
+Chapter \ref{DIA}	& DIA		& I/O and DIAgnostics (also IOM, FLO and TRD) \\		\hline
 Chapter \ref{OBS}	& OBS		& OBServation and model comparison  \\		\hline
-Chapter \ref{ASM}	& ASM		& ASsimilation increment  \\		\hline
-Chapter \ref{MISC}	& ...			& Miscellaneous  topics (DIA, DTA, IOM,   \\
-						&				   & SOL, TRD, FLO...)   \\       \hline
-Chapter \ref{CFG}	&  - 			& predefined configurations  \\		\hline
+Chapter \ref{ASM}	& ASM		& ASsiMilation increment  \\		\hline
+Chapter \ref{MISC}	& SOL		& Miscellaneous  topics (including solvers)  \\       \hline
+Chapter \ref{CFG}	&  - 			& predefined configurations (including C1D) \\		\hline
 \end{tabular} 	
-\caption{	 \label{Tab_chap}
-Organization of Chapters which miminc the one of the model directories. }
 \end{center}	\end{table}
 %--------------------------------------------------------------------------------------------------------------
@@ -141,5 +144,4 @@
 
 $\bullet$ The main modifications from OPA v8 and NEMO/OPA v3.2 are :\\
-\\
 (1) transition to full native \textsc{Fortran} 90, deep code restructuring and drastic 
 reduction of CPP keys; \\
@@ -150,5 +152,5 @@
 coordinate and for the new options for horizontal pressure gradient computation with 
 a non-linear equation of state.}; \\ 
-(4) more choices for the treatment of the free surface: full explicit, split-explicit and filtered. \\
+(4) more choices for the treatment of the free surface: full explicit, split-explicit or filtered schemes. \\
 (5) suppression of the rigid-lid option;\\
 (6) non linear free surface option (associated with the rescaled height coordinate  
@@ -162,18 +164,31 @@
 (12) surface module (SBC) that simplify the way the ocean is forced and include two
 bulk formulea (CLIO and CORE) and which includes an on-the-fly interpolation of input forcing fields\\
-(13) introduction of LIM 3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
+(13) RGB light penetration and optional use of ocean color 
+(14) major changes in the TKE schemes: it now includes a Langmuir cell parameterization  \citep{Axell_JGR02}, 
+the \citet{Mellor_Blumberg_JPO04} surface wave breaking parameterization, and has a time discretization 
+which is energetically consistent with the ocean model equations \citep{Burchard_OM02, Marsaleix_al_OM08}; \\
+(15) tidal mixing parametrisation (bottom intensification) + Indonesian specific tidal mixing \citep{Koch-Larrouy_al_GRL07}; \\
+(16) introduction of LIM-3, the new Louvain-la-Neuve sea-ice model (C-grid rheology and
 new thermodynamics including bulk ice salinity) \citep{Vancoppenolle_al_OM09a, Vancoppenolle_al_OM09b}
 
  \vspace{1cm}
-$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.2 are :\\
-\\
+$\bullet$ The main modifications from NEMO/OPA v3.2 and  v3.3 are :\\
 (1) introduction of a modified leapfrog-Asselin filter time stepping scheme \citep{Leclair_Madec_OM09}; \\
-(2) additional scheme for  iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\
-(3) a rewriting of the bottom boundary scheme, following \citet{Campin_Goosse_Tel99}; \\
-(4) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\
-(5) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\
-(6) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\
-(7) optional application of an assimilation increment (thanks to NEMOVAR project); \\
-(8) introduction of .....    
+(2) additional scheme for iso-neutral mixing \citep{Griffies_al_JPO98}, although it is still a "work in progress"; \\
+(3) a rewriting of the bottom boundary layer scheme, following \citet{Campin_Goosse_Tel99}; \\
+(4) addition of a Generic Length Scale vertical mixing scheme, following \citet{Umlauf_Burchard_JMS03};
+(5) addition of the atmospheric pressure as an external forcing on both ocean and sea-ice dynamics; \\
+(6) addition of a diurnal cycle on solar radiation \citep{Bernie_al_CD07}; \\
+(7) river runoffs added through a non-zero depth, and having its own temperature and salinity; \\
+(8) CORE II normal year forcing set as the default forcing of ORCA2-LIM configuration ; \\
+(9) generalisation of the use of \mdl{fldread} for all input fields (ocean, climatology, sea-ice damping...) 
+(10) addition of an on-line observation and model comparison (thanks to NEMOVAR project); \\
+(11) optional application of an assimilation increment (thanks to NEMOVAR project); \\
+(12) coupling interface adjusted for WRF atmospheric model
+(13) C-grid ice rheology now available fro both LIM-2 and LIM-3 \citep{Bouillon_al_OM09}; \\
+(14) a deep re-writting and simplification of the off-line tracer component (OFF\_SRC) ;  \\
+(15) the merge of passive and active advection and diffusion modules \\
+(16)  Use of the Flexible Configuration Manager (FCM) to build configurations, generate the Makefile and produce the executable ; \\
+(17) Linear-tangent and Adjoint component (TAM) added, phased with v3.0
 
  \vspace{1cm}
